In this lab, we will explore some of R’s functionality with spatial data, with special attention given to the sf package. For more information about sf, you can visit their website. Robin Lovelace’s book Geocomputation with R (available online) is also a really helpful and educational source for learning sf. In fact, much of this lab is just an abbreviated version of that book. For some of the longer examples, it is highly recommended to use R’s scripting functions to run the examples to save on re-typing.

Before starting, remember to create a working directory (e.g. module12). Next download the files for today’s lab from the Canvas page and move them to this directory. You’ll need the following files:

Climate dataset for Western North America: WNAclimate.csv
Temperature dataset for Oregon in shapefile format: oregon.zip
New York state polygon data in a shapefile: NY_Data.zip
Digital elevation map from Switzerland: swiss_dem.grd
A NetCDF file of global monthly air temperature: air.mon.ltm.nc
A NetCDF file of global monthly mean air temperature: air.mon.mean.nc
A dataset of country socioeconomic variables: countries.zip

Make sure to unzip the zip files so that R can access the content. Note that on Windows, you will need to right-click on the file and select ‘Extract files’.

Base R has no structure for spatial data, so you will need to install the following packages (you should have some of these from previous modules):

sf
terra
RColorBrewer
ggplot2
viridis

library(ggplot2)
library(terra)
library(RColorBrewer)
library(sf)
library(viridis)

Intro to `sf`

What is `sf`?

sf is an R package designed to work with spatial data organized as “simple features” (hence, ‘sf’). Mostly, it supersedes the sp package (written by the same people), but it also collapses a lot of other R packages into one. In fact, just a few years ago, if you were to take this course, you would have loaded all of these packages:

library(maptools)
library(rgdal)
library(rgeos)
library(sp)

Now, a simple

library(sf)

will suffice. The sf package is able to provide all the functionality it does because it interfaces with three widely adopted programming standards: PROJ, GDAL, and GEOS. These provide for coordinate reference systems, reading and writing of spatial data, and geometric operations, respectively, but more on this in a moment.

Note that all sf functions are prefixed with st_ (a legacy of this R package’s origins in PostGIS, where ‘st’ means “spatial type”).

What is a simple feature?

A simple feature is, in the words of the sf authors, “a formal standard (ISO 19125-1:2004) that describes how objects in the real world can be represented in computers, with emphasis on the spatial geometry of these objects” (ref). In other words, its structured data that provides information about a location in space, including its shape.

The way that sf chooses to represent simple features in R should be familiar to you because they are just fancy data.frames. To demonstrate this, we’ll load a file of county outlines for North Carolina (this file is included when you install the sf package):

path_to_data <- system.file("shape/nc.shp", package="sf")

north_carolina <- st_read(path_to_data, quiet = TRUE)

north_carolina <- north_carolina[ , c("CNTY_ID", "NAME", "AREA", "PERIMETER")]

north_carolina

## Simple feature collection with 100 features and 4 fields
## Geometry type: MULTIPOLYGON
## Dimension:     XY
## Bounding box:  xmin: -84.32385 ymin: 33.88199 xmax: -75.45698 ymax: 36.58965
## Geodetic CRS:  NAD27
## First 10 features:
##    CNTY_ID        NAME  AREA PERIMETER                       geometry
## 1     1825        Ashe 0.114     1.442 MULTIPOLYGON (((-81.47276 3...
## 2     1827   Alleghany 0.061     1.231 MULTIPOLYGON (((-81.23989 3...
## 3     1828       Surry 0.143     1.630 MULTIPOLYGON (((-80.45634 3...
## 4     1831   Currituck 0.070     2.968 MULTIPOLYGON (((-76.00897 3...
## 5     1832 Northampton 0.153     2.206 MULTIPOLYGON (((-77.21767 3...
## 6     1833    Hertford 0.097     1.670 MULTIPOLYGON (((-76.74506 3...
## 7     1834      Camden 0.062     1.547 MULTIPOLYGON (((-76.00897 3...
## 8     1835       Gates 0.091     1.284 MULTIPOLYGON (((-76.56251 3...
## 9     1836      Warren 0.118     1.421 MULTIPOLYGON (((-78.30876 3...
## 10    1837      Stokes 0.124     1.428 MULTIPOLYGON (((-80.02567 3...

You can summarize this somewhat verbose printout by noting that simple features fit a simple formula:

\[ sf = attributes + geometry + crs \]

This formula also suggests the kinds of ways that you might interact with an sf object by, for example, changing its crs, or filtering based on its attributes (or geometry), or manipulating its geometry.

Attributes

Attributes are properties of a feature. In this case, the features are counties in North Carolina, and their attributes are things like name and area. In an sf data.frame, each feature is a row, and each attribute is a column. In the north_carolina object, for example, the first feature has the name “Ashe” and its county ID is 1825.

Geometry

A very special attribute column is called the geometry (sometimes labeled ‘geom’ or ‘shape’). It consists of a point or set of points (specifically, their coordinates) that define the shape and location of the feature. The simple feature standard includes 17 geometry types, 7 of which are supported by sf: point, multipoint, linestring, multilinestring, polygon, multipolygon, and geometry collection.

Figure 2.2 in Geocomputation with R

As mentioned already, these geometries are just a series of points:

point_one <- st_point(c(0, 3))

point_two <- st_point(c(5, 7))

a_line <- st_linestring(c(point_one, point_two))

If you print these geometries

point_one

## POINT (0 3)

a_line

## LINESTRING (0 3, 5 7)

you see that they are represented as a text string. This is the Well Known Text (WKT) standard for specifying geometries. It tells us what kind of geometry the feature is and lists its x-y coordinates separated by commas.

If you want to know what geometry type your simple feature contains, try:

st_geometry_type(a_line)

## [1] LINESTRING
## 18 Levels: GEOMETRY POINT LINESTRING POLYGON MULTIPOINT ... TRIANGLE

CRS

The final ingredient in a simple feature is its a spatial or coordinate reference system (CRS). A CRS provides two crucial pieces of information: (i) what rule we use to assign coordinates to points and (ii) what datum to use. It is not an exaggeration to say that the CRS is the most important element of a simple feature, for without a CRS, the numbers in the geometry column are just that, numbers, rather than full-blooded spatial coordinates.

Understanding what a coordinate assignment rule does is beyond the scope of this lab, but the datum deserves some attention. In effect, it specifies three things:

the origin or the point on the earth’s surface where the coordinates are POINT (0 0),
the scale of the coordinates, for example, whether we should think of POINT (5 7) as being 5 meters east and seven meters north of the origin, or - worse - 5 feet east and 7 feet north, and
the orientation of the system, or which way is up?

As with the geometries, the standard for representing CRS is WKT, though the easiest way to identify a CRS is to use its EPSG code. To find the EPSG code for a CRS, you can visit this website: spatialreference.org.

The most widely used CRS is the World Geodetic System 84 (WGS 84, a geographic system) whose EPSG code is 4326:

st_crs(4326)

## Coordinate Reference System:
##   User input: EPSG:4326 
##   wkt:
## GEOGCRS["WGS 84",
##     ENSEMBLE["World Geodetic System 1984 ensemble",
##         MEMBER["World Geodetic System 1984 (Transit)"],
##         MEMBER["World Geodetic System 1984 (G730)"],
##         MEMBER["World Geodetic System 1984 (G873)"],
##         MEMBER["World Geodetic System 1984 (G1150)"],
##         MEMBER["World Geodetic System 1984 (G1674)"],
##         MEMBER["World Geodetic System 1984 (G1762)"],
##         MEMBER["World Geodetic System 1984 (G2139)"],
##         ELLIPSOID["WGS 84",6378137,298.257223563,
##             LENGTHUNIT["metre",1]],
##         ENSEMBLEACCURACY[2.0]],
##     PRIMEM["Greenwich",0,
##         ANGLEUNIT["degree",0.0174532925199433]],
##     CS[ellipsoidal,2],
##         AXIS["geodetic latitude (Lat)",north,
##             ORDER[1],
##             ANGLEUNIT["degree",0.0174532925199433]],
##         AXIS["geodetic longitude (Lon)",east,
##             ORDER[2],
##             ANGLEUNIT["degree",0.0174532925199433]],
##     USAGE[
##         SCOPE["Horizontal component of 3D system."],
##         AREA["World."],
##         BBOX[-90,-180,90,180]],
##     ID["EPSG",4326]]

If you are familiar with the PROJ4-string syntax, you can retrieve that from a CRS with:

st_crs(4326)$proj4string

## [1] "+proj=longlat +datum=WGS84 +no_defs"

However, current open standards specified by PROJ and GDAL discourage the use of PROJ4-string syntax in favor of WKT, so it is probably best to get use to the latter now.

Bounding Box

There’s actually one more element to a simple feature, but it is not as vital as the others and is really already implicit in the geometry. That is the bounding box. This is an object defined by the spatial extent of the data: the minimum and maximum x and y coordinates. You can retrieve the bounding box of a simple feature this way:

st_bbox(north_carolina)

##      xmin      ymin      xmax      ymax 
## -84.32385  33.88199 -75.45698  36.58965

There are myriad uses for the bounding box, though we need not dwell on them here.

Read and Write

Reading and writing spatial data, it turns out, is quite the chore. The solution sf relies on is to interface with GDAL, which handles lots of different spatial data types (it’s kinda its whole purpose). Currently supported (vector) spatial data types can be found at GDAL.org. Perhaps the most common spatial data type - because ESRI is a thing - is the shapefile, which has a .shp file extension.

Reading in spatial data

In sf, the function for reading in spatial data is st_read. Here is the nitty-gritty and, perhaps, needlessly verbose version first:

NY8 <- st_read(dsn = "./NY_data/NY8_utm18.shp",
               layer = "NY8_utm18",
               drivers = "ESRI Shapefile")

## options:        ESRI Shapefile 
## Reading layer `NY8_utm18' from data source 
##   `/Users/u0784726/Dropbox/Data/devtools/geog5680/12 Spatial data in R/NY_data/NY8_utm18.shp' 
##   using driver `ESRI Shapefile'
## Simple feature collection with 281 features and 17 fields
## Geometry type: POLYGON
## Dimension:     XY
## Bounding box:  xmin: 358241.9 ymin: 4649755 xmax: 480393.1 ymax: 4808545
## Projected CRS: WGS 84 / UTM zone 18N

dsn stands for “data source name” and specifies where the data is coming from, whether a file directory, a database, or something else. layer is the layer in the data source to be read in. Finally, drivers tells GDAL what format the file is in or what structure it has, so it knows how to correctly interpret the file. All of this information is printed to the console when you execute st_read.

In this case, we are using a simple ESRI shapefile, so the data source and layer are basically the same thing. Furthermore, sf is good at guessing the driver based on the file extension, so the driver does not normally need to be specified. Hence, we could just as well have written:

NY8 <- st_read("./NY_data/NY8_utm18.shp")

## Reading layer `NY8_utm18' from data source 
##   `/Users/u0784726/Dropbox/Data/devtools/geog5680/12 Spatial data in R/NY_data/NY8_utm18.shp' 
##   using driver `ESRI Shapefile'
## Simple feature collection with 281 features and 17 fields
## Geometry type: POLYGON
## Dimension:     XY
## Bounding box:  xmin: 358241.9 ymin: 4649755 xmax: 480393.1 ymax: 4808545
## Projected CRS: WGS 84 / UTM zone 18N

And here’s what this looks like:

Converting non-spatial data to simple features

Sometimes you have spatial data, but it is not in a spatial data format. Usually, this means you have a table or spreadsheet with columns for the x and y coordinates.

wna_climate <- read.csv("./WNAclimate.csv")

head(wna_climate)

##   WNASEQ     LONDD   LATDD ELEV totsnopt annp Jan_Tmp Jul_Tmp
## 1      1 -107.9333 50.8736  686  78.7869  326   -13.9    18.8
## 2      2 -105.2670 55.2670  369 145.3526  499   -21.3    16.8
## 3      3 -102.5086 41.7214 1163  42.6544  450    -4.2    23.3
## 4      4 -110.2606 44.2986 2362 255.1009  489   -10.9    14.1
## 5      5 -114.1500 59.2500  880 164.8924  412   -23.9    14.4
## 6      6 -120.6667 57.4500  900 141.9260  451   -17.5    13.8

This can be converted to a simple feature using the st_as_sf function like so:

wna_climate <- st_as_sf(wna_climate, 
                        coords = c("LONDD", "LATDD"),
                        crs = 4326)

wna_climate

## Simple feature collection with 2012 features and 6 fields
## Geometry type: POINT
## Dimension:     XY
## Bounding box:  xmin: -138 ymin: 29.8333 xmax: -100 ymax: 60
## Geodetic CRS:  WGS 84
## First 10 features:
##    WNASEQ ELEV totsnopt annp Jan_Tmp Jul_Tmp                  geometry
## 1       1  686  78.7869  326   -13.9    18.8 POINT (-107.9333 50.8736)
## 2       2  369 145.3526  499   -21.3    16.8   POINT (-105.267 55.267)
## 3       3 1163  42.6544  450    -4.2    23.3 POINT (-102.5086 41.7214)
## 4       4 2362 255.1009  489   -10.9    14.1 POINT (-110.2606 44.2986)
## 5       5  880 164.8924  412   -23.9    14.4     POINT (-114.15 59.25)
## 6       6  900 141.9260  451   -17.5    13.8   POINT (-120.6667 57.45)
## 7       7 1100 183.4187  492   -18.8    13.2 POINT (-119.7167 56.7167)
## 8       8 1480 191.5657  606   -11.0    12.8    POINT (-114.6 50.7667)
## 9       9  651 144.9015  443   -22.4    15.3 POINT (-122.1667 59.5167)
## 10     10  725 151.0778  455   -23.5    15.4    POINT (-112.1 57.7667)

The function just needs to know what columns the x and y coordinates are in and what CRS they are specified in. And here’s what it looks like:

Writing spatial data

The sf function for writing simple features to disk is st_write. It is almost an exact mirror of st_read, but it also requires that you specify the simple feature object in your R environment that you want to write to disk. If the layer already exists, you will need to specify delete_layer = TRUE.

st_write(obj = wna_climate,
         dsn = "./wnaclim.shp",
         layer = "wnaclim",
         drivers = "ESRI Shapefile")

or, more simply:

st_write(wna_climate, dsn = "./wnaclim.shp")

CRS operations

The cardinal rule for working with any spatial data is to make sure all of it is in the same CRS. This ensures that any analysis which combines multiple sources is correctly comparing values at the same locations. Never ever ever ever do anything with your data until you are sure you’ve got the CRS right.

Check CRS

The st_crs() function allows you to quickly check the CRS for any object.

st_crs(NY8)

## Coordinate Reference System:
##   User input: WGS 84 / UTM zone 18N 
##   wkt:
## PROJCRS["WGS 84 / UTM zone 18N",
##     BASEGEOGCRS["WGS 84",
##         DATUM["D_unknown",
##             ELLIPSOID["WGS84",6378137,298.257223563,
##                 LENGTHUNIT["metre",1,
##                     ID["EPSG",9001]]]],
##         PRIMEM["Greenwich",0,
##             ANGLEUNIT["Degree",0.0174532925199433]]],
##     CONVERSION["UTM zone 18N",
##         METHOD["Transverse Mercator",
##             ID["EPSG",9807]],
##         PARAMETER["Latitude of natural origin",0,
##             ANGLEUNIT["Degree",0.0174532925199433],
##             ID["EPSG",8801]],
##         PARAMETER["Longitude of natural origin",-75,
##             ANGLEUNIT["Degree",0.0174532925199433],
##             ID["EPSG",8802]],
##         PARAMETER["Scale factor at natural origin",0.9996,
##             SCALEUNIT["unity",1],
##             ID["EPSG",8805]],
##         PARAMETER["False easting",500000,
##             LENGTHUNIT["metre",1],
##             ID["EPSG",8806]],
##         PARAMETER["False northing",0,
##             LENGTHUNIT["metre",1],
##             ID["EPSG",8807]],
##         ID["EPSG",16018]],
##     CS[Cartesian,2],
##         AXIS["(E)",east,
##             ORDER[1],
##             LENGTHUNIT["metre",1,
##                 ID["EPSG",9001]]],
##         AXIS["(N)",north,
##             ORDER[2],
##             LENGTHUNIT["metre",1,
##                 ID["EPSG",9001]]]]

You can also check the EPSG code (if specified):

st_crs(NY8)$epsg

## [1] NA

st_crs(wna_climate)$epsg

## [1] 4326

And you can get the name of a CRS this way:

format(st_crs(NY8))

## [1] "WGS 84 / UTM zone 18N"

Set CRS

There are two methods to set the CRS for a spatial object: st_crs<- and st_set_crs.

wna_climate <- st_set_crs(wna_climate, 4326)

st_crs(wna_climate) <- 4326

# st_crs(wna_climate)

Note: this should only be used when the simple feature is missing a CRS and you know what it is. It is NOT for re-projecting the sf object to a new coordinate system.

Reprojecting CRS

The st_transform() function allows you to project your sf object to a new CRS. This is particularly useful if you have multiple data sources with different original coordinate systems.

# st_crs(NY8)

NY8 <- st_transform(NY8, crs = 4326)

# st_crs(NY8)

As a reminder: when you read in spatial data, the first thing you should use is st_crs to check the CRS and st_transform to re-project if necessary.

Attribute operations

The attribute part of a sf object is a data.frame, so you can use all the methods we have previously looked at for data manipulation in working with attributes.

oregon_tann <- read_sf("./oregon/oregontann.shp")

class(oregon_tann)

## [1] "sf"         "tbl_df"     "tbl"        "data.frame"

If you enter the name of an sf object, it will print the first few rows of the attribute table:

oregon_tann

## Simple feature collection with 92 features and 4 fields
## Geometry type: POINT
## Dimension:     XY
## Bounding box:  xmin: -124.567 ymin: 42.05 xmax: -116.967 ymax: 46.15
## CRS:           NA
## # A tibble: 92 × 5
##    elevation  tann coords_x1 coords_x2          geometry
##        <int> <dbl>     <dbl>     <dbl>           <POINT>
##  1       846   9.6     -121.      44.9 (-120.717 44.917)
##  2        96  12.5     -120.      45.7   (-120.2 45.717)
##  3       543  11.1     -123.      42.2 (-122.717 42.217)
##  4         2  10.3     -124.      46.2  (-123.883 46.15)
##  5      1027   7.6     -118.      44.8 (-117.817 44.833)
##  6      1050   8.4     -118.      44.8 (-117.833 44.783)
##  7        24  10.8     -124.      43.1 (-124.383 43.117)
##  8      1097   7.7     -121.      44.1 (-121.317 44.067)
##  9       999   9.5     -118.      43.9 (-118.167 43.917)
## 10        18  11.2     -122.      45.6  (-121.95 45.633)
## # ℹ 82 more rows

Select Columns

# get elevation and tann columns

# method 1
oregon_tann2 <- oregon_tann[ , c("elevation", "tann")]

# method 2
oregon_tann2 <- subset(oregon_tann, select = c(elevation, tann))

names(oregon_tann)

## [1] "elevation" "tann"      "coords_x1" "coords_x2" "geometry"

names(oregon_tann2)

## [1] "elevation" "tann"      "geometry"

Notice this very important difference between regular data.frames and sf data.frames: when you subset by columns, even though you do not explicitly state that you want to keep the geometry column, it keeps that column anyway. In this sense, the geometry column is said to be “sticky.”

Filter Rows

Subsetting the data by rows works in the same way as before. So we can carry out conditional selection of locations by using the usual comparison operators (<, <=, ==, !=, >=, >). For example, to select only the points above 1000 m elevation in the Oregon data set:

# get features above 1000 meters

# method 1
oregon_tann3 <- oregon_tann[oregon_tann$elevation > 1000, ]

# method 2
oregon_tann3 <- subset(oregon_tann, subset = elevation > 1000)

Add Column

New variables can easily be appended to an existing sf object using the following notation:

# method 1
oregon_tann$rando <- runif(n = nrow(oregon_tann))

# method 2
oregon_tann[, "rando"] <- runif(n = nrow(oregon_tann))

names(oregon_tann)

## [1] "elevation" "tann"      "coords_x1" "coords_x2" "geometry"  "rando"

Extract Column

If you need to extract any variable from a sf object to a standard R vector, you can again use the standard notation. Note that if you use [,] to specify the columns, you need to add drop = TRUE to remove the geometry:

# method 1
elevaton <- oregon_tann$elevation

# method 2
# if you don't specify drop = TRUE, it'll keep the sticky geometry column
elevation <- oregon_tann[ , "elevation", drop = TRUE] 

elevation[1:10]

##  [1]  846   96  543    2 1027 1050   24 1097  999   18

Get Geometry

If you need only the geometry (the set of coordinates, or vector definitions), these can be extracted as follows:

# method 1
geometry <- st_geometry(oregon_tann)

# method 2
geometry <- oregon_tann$geometry

geometry

## Geometry set for 92 features 
## Geometry type: POINT
## Dimension:     XY
## Bounding box:  xmin: -124.567 ymin: 42.05 xmax: -116.967 ymax: 46.15
## CRS:           NA
## First 5 geometries:

## POINT (-120.717 44.917)

## POINT (-120.2 45.717)

## POINT (-122.717 42.217)

## POINT (-123.883 46.15)

## POINT (-117.817 44.833)

Drop Geometry

In case you just want the attributes, not the geometry:

attributes <- st_drop_geometry(oregon_tann)

head(attributes)

## # A tibble: 6 × 5
##   elevation  tann coords_x1 coords_x2 rando
##       <int> <dbl>     <dbl>     <dbl> <dbl>
## 1       846   9.6     -121.      44.9 0.969
## 2        96  12.5     -120.      45.7 0.706
## 3       543  11.1     -123.      42.2 0.444
## 4         2  10.3     -124.      46.2 0.493
## 5      1027   7.6     -118.      44.8 0.591
## 6      1050   8.4     -118.      44.8 0.554

Note: this is actually a special sort of data.frame called a tibble. Not important to know about here, but does print slightly differently.

Spatial operations

Spatial operations are like attribute operations, but they work with the geometry column rather than the attributes. There are loads of these functions, but will just review some of the more important ones here.

Spatial Filter

This is probably the biggest one. Basically, you are taking one geometry and using it to filter other geometries. To demonstrate this, first we’ll make some random points in the north_carolina simple feature. Well, first-first, we need to project the simple features, since sf will protest if you try to do spatial operations on longitude and latitude, as several of these methods require the calculation of distances between locations.

north_carolina <- st_transform(north_carolina, crs = 26918)

Now use st_sample to generate the random points:

set.seed(1234)

random_pnts <- st_sample(north_carolina, size = 500)

random_pnts <- st_as_sf(random_pnts)

Now, we can use one geometry to filter out a second one. To obtain just the points in, say, Pasquotank County, we first subset the North Carolina sf object to extract only this county:

pasquotank <- subset(north_carolina, NAME == "Pasquotank")

Then use the st_filter() function with the county polygon to get only the points located in that polygon:

filtered_pnts <- st_filter(random_pnts, pasquotank)

Now, you know where Pasquotank County is!

Topological Relations

Internally, st_filter assumes a “topological” or spatial relationship defined by what the sf authors refer to as spatial predicate (.predicate). By default, st_intersects works to find the geometry of one object located within another. We can, however, specify other spatial relationships. For example, to get all the points outside Pasquotank:

filtered_pnts <- st_filter(random_pnts, pasquotank, .predicate = st_disjoint)

Another useful predicate is st_is_within_distance, which requires that you pass an additional distance (dist) argument to the filter. The dist argument is in units specified by the CRS, in this case meters.

filtered_pnts <- st_filter(random_pnts, 
                           pasquotank, 
                           .predicate = st_is_within_distance,
                           dist = 50000)

Geometric operations

With spatial operations, the geometry is preserved (mostly). With geometric operations, the whole point is to manipulate the geometry. Again, we are just going to hit the highlights. It is worth emphasizing that these operations will often behave differently depending on the geometry type.

Centroid

the_heart_of_pasquotank <- st_centroid(pasquotank)

## Warning: st_centroid assumes attributes are constant over geometries

Buffer

the_heft_of_pasquotank <- st_buffer(pasquotank, dist = 50000)

Union

This one merges geometries and dissolves interior borders when applied to polygons.

north_carolina_boundary <- st_union(north_carolina)

Cast

To cast a geometry is to change it from one geometry type to another. For example, to convert the boundary of North Carolina to points (the vertices of the polygon):

north_carolina_points <- st_cast(north_carolina_boundary, "POINT")

If we convert to a LINESTRING object, this acts to separate out the individual polygons:

north_carolina_lines <- st_cast(north_carolina_boundary, "MULTILINESTRING")

north_carolina_lines <- st_cast(north_carolina_lines, "LINESTRING")

If you can’t tell, it was broken into six lines: one for the mainland, and the other five for the ecological (and cultural) disaster known as the Outer Banks.

Plotting

`graphics`

To make simple plots of an sf object, you can use R’s base function plot():

plot(oregon_tann2)

Notice that it creates separate plots for each attribute. If you would prefer to plot the geometry itself, you have to say so explicitly.

plot(st_geometry(oregon_tann2))

`ggplot2`

One of the easiest ways to improve on these base plots is to use ggplot2. This contains a a special plotting geometry, geom_sf, designed to work with sf objects. Here, we’ll use a subset of polygons from the NY8 data to illustrate how this works. (Note that geom_sf refers to a ggplot2 geometry, not a sf geometry.)

binghamton <- subset(NY8, AREANAME == "Binghamton city")

We can now plot this by calling the ggplot() function and adding the sf object with geom_sf:

ggplot() + 
  geom_sf(data = binghamton) +
  theme_bw()

Multiple Geometries

Multiple layers can be added to a plot by adding additional geom_sf functions. Here, we first create a new sf object containing Binghamton and it’s neighboring polygons, then create some random points for plotting:

sf::sf_use_s2(FALSE)

bingies_neighbors <- st_filter(NY8, binghamton)

random_pnts <- st_sample(bingies_neighbors, size = 25)

random_pnts <- st_as_sf(random_pnts)

Now we can plot these: first the larger set of polygons, then Binghamton City and finally the points:

ggplot() + 
  geom_sf(data = bingies_neighbors) +
  geom_sf(data = binghamton, fill = "blue") +
  geom_sf(data = random_pnts, color = "darkgreen") +
  theme_bw()

Plotting attributes

We can create thematic maps by specifying the name of a variable in the geom_sf() function:

names(binghamton)

##  [1] "AREANAME"   "AREAKEY"    "X"          "Y"          "POP8"      
##  [6] "TRACTCAS"   "PROPCAS"    "PCTOWNHOME" "PCTAGE65P"  "Z"         
## [11] "AVGIDIST"   "PEXPOSURE"  "Cases"      "Xm"         "Ym"        
## [16] "Xshift"     "Yshift"     "geometry"

ggplot() + 
  geom_sf(data = binghamton, aes(fill = POP8)) +
  theme_bw()

Manual Color Scale

Here, we will use the viridis color scale, which is colorblind safe. This comes with several color palette options.

ggplot() + 
  geom_sf(data = binghamton, aes(fill = PEXPOSURE)) +
  scale_fill_viridis(option = "viridis") +
  theme_bw()

ggplot() + 
  geom_sf(data = binghamton, aes(fill = PEXPOSURE)) +
  scale_fill_viridis(option = "magma") +
  theme_bw()

Coordinates

By default, geom_sf transforms all sf objects to WGS84 (or latitude and longitude), but you can change this with coord_sf. This takes an argument datum that can be used to specify a different projection. Here we plot the Binghamton data using a UTM projection (zone 18N = EPSG code 26918). Note the change in both the projection of the data, and the axes:

ggplot() + 
  geom_sf(data = binghamton, aes(fill = PEXPOSURE)) +
  scale_fill_viridis(option = "viridis") +
  coord_sf(datum = 26918) +
  theme_bw()

You can also use this to zoom in on different parts of the map.

ggplot() + 
  geom_sf(data = binghamton, aes(fill = PEXPOSURE)) +
  scale_fill_viridis(option = "viridis") +
  coord_sf(xlim = c(-75.93, -75.88), ylim = c(42.09, 42.13)) +
  theme_bw()

Rasters

Up till now, we have been working with vector spatial data. These are geometries composed of points defined by their coordinates. An alternative form of spatial data is known as a raster. This is gridded data. It takes the form of a rectangle composed of squares of equal size, which are sometimes called ‘cells’ or ‘pixels’. Each cell stores some kind of value.

This simplifies the geometry, which can be specified by two pieces of information: the spatial extent of the raster and the resolution of the cells. Here we create a blank raster with 10 rows and 10 columns using the rast() function, and assign random values to each cell:

r <- rast(nrow = 10, ncol = 10)

r[] <- runif(n = 100)

r

## class       : SpatRaster 
## dimensions  : 10, 10, 1  (nrow, ncol, nlyr)
## resolution  : 36, 18  (x, y)
## extent      : -180, 180, -90, 90  (xmin, xmax, ymin, ymax)
## coord. ref. : lon/lat WGS 84 
## source(s)   : memory
## name        :      lyr.1 
## min value   : 0.01260905 
## max value   : 0.98447369

rast objects can be plotted using the base plot() command:

plot(r)

The terra package offers a wide array of functions for dealing with gridded data, including the ability to read from many widely used file formats, like remote sensing images (e.g. GeoTiffs), NetCDF, and HDF formats. We will use it here to work with gridded air temperature data (air.mon.ltm.nc) from the NCAR NCEP reanalysis project. This is the long term means for each month from 1981-2010. The file has 12 layers (one per month) and one variable (air).

Read and Write Rasters

To read in gridded data, use the rast() function.

air_temp <- rast("./air.mon.ltm.nc")

## Warning: [rast] unknown extent

air_temp

## class       : SpatRaster 
## dimensions  : 73, 144, 24  (nrow, ncol, nlyr)
## resolution  : 1, 1  (x, y)
## extent      : 0, 144, 0, 73  (xmin, xmax, ymin, ymax)
## coord. ref. :  
## sources     : air.mon.ltm.nc://air  (12 layers) 
##               air.mon.ltm.nc://valid_yr_count  (12 layers) 
## varnames    : air 
##               valid_yr_count 
## names       : air_1, air_2, air_3, air_4, air_5, air_6, ...

When we print the rast object created, the second line of the output lists the dimensions of the data. Note that here, this has 73 rows, 144 columns and 24 layers (each representing a different variable)

In this case, rast has not set the spatial extent of the data correctly, so we can do that by hand. The NCAR data span from 0-360 longitude and -90 to 90 latitude:

set.ext(air_temp, value = c(0, 360, -90, 90))

ext(air_temp)

## SpatExtent : 0, 360, -90, 90 (xmin, xmax, ymin, ymax)

You can access any of the layers using R’s list notation (e.g. rast[[1]]). To extract the first layer (here, January air temperature):

jan_temp = air_temp[[1]]

jan_temp

## class       : SpatRaster 
## dimensions  : 73, 144, 1  (nrow, ncol, nlyr)
## resolution  : 2.5, 2.465753  (x, y)
## extent      : 0, 360, -90, 90  (xmin, xmax, ymin, ymax)
## coord. ref. :  
## source      : air.mon.ltm.nc://air 
## varname     : air 
## name        : air_1

We can write rast objects back to file using writeRaster() (I’ll bet you never thought it would be called that). Here we write out to a TIFF format. You can see the full list of available formats for reading and writing by running the writeFormats() function in the console.

writeRaster(jan_temp, 
            filename = "./jan_temp.tif",
            overwrite = TRUE)

Raster CRS

Set CRS:

crs(jan_temp) <- "EPSG:4326"

Again, this should not be used to change the CRS, only set it.

Get CRS:

crs(jan_temp, proj = TRUE)

## [1] "+proj=longlat +datum=WGS84 +no_defs"

Also, note that crs is for rastersrastobjects,st_crs` for vectors.

Transform CRS. Note that terra can also uses the PROJ4-string syntax. It’s a holdover from its original development:

weird_crs <- crs("+proj=tmerc +lat_0=0 +lon_0=15 +k=0.999923 +x_0=5500000 +y_0=0 +ellps=GRS80 +units=m +no_defs")

jan_temp_weird_crs <- project(jan_temp, weird_crs)

crs(jan_temp_weird_crs, proj = TRUE)

## [1] "+proj=tmerc +lat_0=0 +lon_0=15 +k=0.999923 +x_0=5500000 +y_0=0 +ellps=GRS80 +units=m +no_defs"

Basic Plotting

jan_temp is a rast object and has information about grid spacing, coordinates etc. Note that the description of the object tells you whether it is held in memory (small raster files) or on disk.

plot(jan_temp, main = "NCEP NCAR January LTM Tair")

And you should be able to see the outline of the continents. We can convert this to the more commonly used (and UK-centric :) ) -180 to 180 by the function rotate(). We’ll also use a different color palette and overlay country polygons. You can use sf objects for this, or use the terra package own vector format (vect). We’ll use that here, as it has some advantages for spatial overlays. To read in a shapefile in this format, use the vect function:

jan_temp = rotate(jan_temp)

# using RColorBrewer
my.pal <- brewer.pal(n = 9, name = "OrRd")

plot(jan_temp, 
     main = "NCEP NCAR January LTM Tair", 
     col = my.pal)

countries <- vect("./ne_50m_admin_0_countries/ne_50m_admin_0_countries.shp")

plot(countries, add = TRUE)

To see other color palettes in the RColorBrewer package, run display.brewer.all() in the console. You can find out more details and explore visualizations with these palettes here.

Summary Statistics

The function cellStats() can be used to calculate most summary statistics for a raster layer. So to get the mean global temperature (and standard deviation):

global(jan_temp, mean)

##           mean
## air_1 3.546352

global(jan_temp, sd)

##             sd
## air_1 19.63948

Subset Rasters

If we want to use only a subset of the original raster layer, the function crop() will extract only the cells in a given region. This can be defined using another raster object or Spatial* object, or by defining an extent object:

# extent method
canada_ext <- ext(c(xmin = -142, 
                    xmax = -52, 
                    ymin = 41,
                    ymax = 84))

canada_air_temp <- crop(jan_temp, canada_ext)

If we extract the polygon corresponding to the outline of Canada, we can use that insteadL

canada <- countries[countries$NAME == "Canada", ]

canada_air_temp <- crop(jan_temp, canada)

# plot
plot(canada_air_temp, main = "NCEP NCAR January LTM Tair", col = my.pal)

plot(canada, add = TRUE)

Note that crop subsets the original raster to the extent of Canada’s borders, rather than to the borders themselves. This is because rasters are always rectangular. You can ‘hide’ the values of raster cells outside of a polygon by using the mask function. The raster has to be rectangular, so this does not remove the cells outside the polygon. Rather, it sets their value to NA.

canada_air_temp <- mask(canada_air_temp, mask = canada)

# plot
plot(canada_air_temp, main = "NCEP NCAR January LTM Tair", col = my.pal)

plot(canada, add = TRUE)

Extract Data

Values can be extracted from individual locations (or sets of locations) using extract(). This can take a set of coordinates in matrix form, or use a Spatial* object. To get the January temperature of Salt Lake City:

extract(jan_temp, cbind(-111.9,40.76))

##      air_1
## 1 -6.01876

We created a simple feature object earlier with the location of samples in Western North America (wna_climate). We can now use this, and the raster layer to get the January temperature for all locations.

wna_air_temp_df <- extract(jan_temp, 
                           wna_climate, 
                           method = 'bilinear',
                           df = TRUE) 

head(wna_air_temp_df)

##   ID      air_1
## 1  1  -9.826717
## 2  2 -18.532247
## 3  3  -3.518785
## 4  4  -7.644527
## 5  5 -19.814369
## 6  6 -13.629312

df = TRUE tells the function to return the extracted values as a data.frame, which has two columns the raster cell ID and the value in that cell.

This same approach allows you to extract pixels by polygon overlays.

china <- countries[countries$NAME == "China", ]

china_air_temp_df <- extract(jan_temp, china, df = TRUE)

head(china_air_temp_df)

##   ID     air_1
## 1  1 -23.21633
## 2  1 -23.51869
## 3  1 -22.07151
## 4  1 -20.61807
## 5  1 -23.53544
## 6  1 -24.09268

Note that the first column is an ID corresponding to the polygon that was used. When this function is used with a set of polygons, the output is in a list, but we can retrieve whatever we want from that list.

two_countries <- rbind(china, canada)

two_countries_tjan <- extract(jan_temp, two_countries)

head(two_countries_tjan)

##   ID     air_1
## 1  1 -23.21633
## 2  1 -23.51869
## 3  1 -22.07151
## 4  1 -20.61807
## 5  1 -23.53544
## 6  1 -24.09268

And we can make a quick plot with ggplot2 to show the two distributions of temperature:

library(ggplot2)
library(dplyr)

## Warning: package 'dplyr' was built under R version 4.1.2

## 
## Attaching package: 'dplyr'

## The following objects are masked from 'package:terra':
## 
##     intersect, union

## The following objects are masked from 'package:stats':
## 
##     filter, lag

## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union

two_countries_tjan %>%
  mutate(NAME = ifelse(ID == 1, "China", "Canada")) %>%
  ggplot(aes(x = air_1, fill = NAME)) +
  geom_histogram(position = 'identity', alpha = 0.75)

## `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.

The extract() function also takes an argument fun. This allows you to calculate a summary statistic for each set of pixels that is extracted (i.e. one per polygon). Here, we’ll use this with countries to get an average value of January temperature. We add this back as a new column in the countries object, and then plot it:

countries$Jan_Tmp <- extract(jan_temp, countries, fun = mean)[, 'air_1']

countries_sf <- st_as_sf(countries)

ggplot(countries_sf) +
  geom_sf(aes(fill = Jan_Tmp)) +
  scale_fill_viridis(option = "inferno") +
  labs(fill = "Temperature",
       title = "Country average January temperature") + 
  theme_bw()

Raster Stacks

A useful extension to the basic raster functions is the use of stacks. These are a stack of raster layers which represent different variables, but have the same spatial extent and resolution. There’s nothing special that you need to do here - when we originally read in the air temperature data, the rast object contained all 24 layers from the NetCDF file. This included 12 monthly layers and 12 layers indicating data quality. We’ll re-read this, but this time only include the 12 monthly layers from the NetCDF file, and then work with this. We read these in with rast(), specifying the layers with lyrs=. We also set the extent and rotate the data.

air_temp <- rast("./air.mon.ltm.nc", lyrs = 1:12)

## Warning: [rast] unknown extent

crs(air_temp) <- "EPSG:4326"

set.ext(air_temp, value = c(0, 360, -90, 90))

air_temp = rotate(air_temp)

we can see that this has 12 layers, each with 280 cells and the extent, etc. The names attributed to each layer are often unreadable, so we can add our own names:

names(air_temp) <- paste("TAS", month.abb, sep = "_")

names(air_temp)

##  [1] "TAS_Jan" "TAS_Feb" "TAS_Mar" "TAS_Apr" "TAS_May" "TAS_Jun" "TAS_Jul"
##  [8] "TAS_Aug" "TAS_Sep" "TAS_Oct" "TAS_Nov" "TAS_Dec"

And now you can also pull out rasters by name:

# method 1
jan_temp <- air_temp$TAS_Jan

# method 2
jan_temp <- air_temp[["TAS_Jan"]]

A useful feature when working with stacks is that any of the functions we used previously with one layer will be used across all layers when applied to the stack. The plot() function, for example, returns a grid with one plot per layer. Setting the range argument ensures that all figures use the same range of colors:

plot(air_temp, 
     col = my.pal, 
     type = 'continuous',
     range = c(-40, 40))

Adding a shapefile (or other spatial information) is a little more complex. We create a simple function to plot the country borders, then include this as an addfun in the call to plot():

addBorder = function(){ plot(as_Spatial(countries), add = TRUE) }
addBorder = function(){ lines(vect) }

plot(air_temp, 
     col = my.pal, 
     type = 'continuous',
     breaks = seq(-35, 40, by = 5), 
     fun = function() lines(countries))

The cellStats() function now returns the mean (or other statistic) for all layers, allowing a quick look at the seasonal cycle of average air temperature.

tavg <- global(air_temp, mean)

plot(1:12, tavg$mean, 
     type = 'l', 
     xlab = "Month", 
     ylab = "Avg T (C)")

And we can do the same for an individual location using extract(). We’ll convert this to a dataframe and plot using ggplot2:

slc.tavg <- t(extract(air_temp, cbind(-111.9,40.76)))
plot_df <- data.frame(month = 1:12,
                      tavg = slc.tavg[, 1])
ggplot(plot_df, aes(x = month, y = tavg)) +
  geom_line() +
  scale_x_continuous("Month") +
  scale_y_continuous("Deg C") +
  ggtitle("SLC Temperatures (LTM)") +
  theme_bw()

Exercises

The exercise for the module will get you to make some simple maps with new datasets. You should submit the results as an R script with the commands you used, and a Word (or equivalent) with any results or figures or as an html page generated from an R Markdown document

Exercise 1

In the zipfile countries.zip is a global shapefile with various socio-economic indicators for different countries. Load this file into R and make plots of any two of the following variables (the variable names are given in brackets). Try different color scales and transformations of the data to get the most informative maps

Median GDP: (gdp_md_est)
Population: (pop_est)
Income group: (income_grp)

Exercise 2

The NetCDF file air.mon.mean.nc contains air temperature data from the NCAR NCEP project, but as mean monthly temperature for every year between 1948 and the present. Using the functions introduced in this lab, read in the data and make a dataset with the globally averaged temperature for every layer in the file (i.e. from January 1948 to present). Use this data to make a line plots, either using base R or ggplot2

GEOG 5680 6680 12 Spatial data in R

Simon Brewer and Blake Vernon Geography and Anthropology Departments University of Utah

31 May, 2023

Intro to sf

What is sf?